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Hi, i would suggest to include an option to restrict the coordinate freedom of some selected atoms. It would belong to the System class, (similarly to distance constrain) and could be set for example with a CoordConstraint(int atom_index,bool fix_x,bool fix_y,bool fix_z) function.
It would influence the Force calculation by setting the constrained components to zero and in the integrator or in the optimizer the steps for constrained components are skipped.
(So far it is possible to mimic the full coordinate constraint with very large mass, which is good as a dirty solution.)
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